Identification of crucial genes of pediatric inflammatory bowel disease in remission by protein-protein interaction network and module analyses.

Abstract

Although the main treatments of inflammatory bowel disease (IBD) aim at the induction and maintenance of clinical remission, several studies have demonstrated inflammation still present in clinical remission. The goal of this study was to analyze the gene expression profiles between the pediatric IBD and control samples, aiming to further investigate the underlying therapeutic target in remission. Gene expression profiles data of GSE33943 were downloaded from Gene Expression Omnibus, which included 45 pediatric IBD samples and 13 control samples. The differentially expressed genes (DEGs) between IBD and control samples were identified by LIMMA package in R and the function of DEGs were predicted by Gene Ontology and KEGG pathway enrichment analyses using GeneAnswer package. Furthermore, a protein-protein interaction (PPI) network was constructed through the STRING database and functional module was obtained using ClusterONE. A total of 224 DEGs were screened between IBD and control samples. These DEGs (e.g. up-regulated FAS and down-regulated CCL5) were mainly enriched in cytokine‒cytokine receptor interaction and chemokine signaling pathway. In addition, some hub genes (e.g. up-regulated PSMA2 and PSMA6) were obtained through PPI network and functional module. These two genes were involved in Proteasome alpha-subunit and conserved site by functional module analysis. The immune and Proteasome mechanisms are still active during remission and FAS, PMSF6 and PMSF2 may be underlying targets for therapy of this disease.